diff options
Diffstat (limited to 'src/python')
20 files changed, 317 insertions, 109 deletions
diff --git a/src/python/doc/_templates/layout.html b/src/python/doc/_templates/layout.html index fe64fb3d..2f2d9c72 100644 --- a/src/python/doc/_templates/layout.html +++ b/src/python/doc/_templates/layout.html @@ -56,12 +56,16 @@ </a></p> {%- endif %} {%- endblock %} - <h2><a href="index.html">GUDHI</a></h2> - <h2><a href="fileformats.html">File formats</a></h2> - <h2><a href="installation.html">GUDHI installation</a></h2> - <h2><a href="citation.html">Acknowledging the GUDHI library</a></h2> - <h2><a href="genindex.html">Index</a></h2> - <h2><a href="examples.html">Examples</a></h2> + <b> + <ul style="list-style-type:circle;"> + <li><a href="index.html">Modules</a></li> + <li><a href="installation.html">Installation</a></li> + <li><a href="examples.html">Examples</a></li> + <li><a href="fileformats.html">File formats</a></li> + <li><a href="citation.html">Acknowledging</a></li> + <li><a href="genindex.html">Index</a></li> + </ul> + </b> {%- if sidebars != None %} {#- new style sidebar: explicitly include/exclude templates #} {%- for sidebartemplate in sidebars %} diff --git a/src/python/doc/examples.rst b/src/python/doc/examples.rst index edbc2f72..a42227e3 100644 --- a/src/python/doc/examples.rst +++ b/src/python/doc/examples.rst @@ -16,6 +16,9 @@ Examples * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>` + * :download:`plot_simplex_tree_dim012.py <../example/plot_simplex_tree_dim012.py>` + * :download:`plot_rips_complex.py <../example/plot_rips_complex.py>` + * :download:`plot_alpha_complex.py <../example/plot_alpha_complex.py>` * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>` * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` diff --git a/src/python/doc/index.rst b/src/python/doc/index.rst index 1ef08096..c36a578f 100644 --- a/src/python/doc/index.rst +++ b/src/python/doc/index.rst @@ -1,5 +1,5 @@ -GUDHI Python module documentation -################################# +GUDHI Python modules documentation +################################## .. figure:: ../../doc/common/Gudhi_banner.png diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 7699a5bb..54504413 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -40,6 +40,20 @@ To build the GUDHI Python module, run the following commands in a terminal: cd python make +.. note:: + + :code:`make python` (or :code:`make` in python directory) is only a + `CMake custom targets <https://cmake.org/cmake/help/latest/command/add_custom_target.html>`_ + to shortcut :code:`python setup.py build_ext --inplace` command. + No specific other options (:code:`-j8` for parallel, or even :code:`make clean`, ...) are + available. + But one can use :code:`python setup.py ...` specific options in the python directory: + +.. code-block:: bash + + python setup.py clean --all # Clean former compilation + python setup.py build_ext -j 8 --inplace # Build in parallel + GUDHI Python module installation ================================ @@ -59,6 +73,17 @@ Or install it definitely in your Python packages folder: # May require sudo or administrator privileges make install +.. note:: + + :code:`make install` is only a + `CMake custom targets <https://cmake.org/cmake/help/latest/command/add_custom_target.html>`_ + to shortcut :code:`python setup.py install` command. + It does not take into account :code:`CMAKE_INSTALL_PREFIX`. + But one can use :code:`python setup.py install ...` specific options in the python directory: + +.. code-block:: bash + + python setup.py install --prefix /home/gudhi # Install in /home/gudhi directory Test suites =========== diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst index b2124fdd..2de99252 100644 --- a/src/python/doc/persistence_graphical_tools_user.rst +++ b/src/python/doc/persistence_graphical_tools_user.rst @@ -20,6 +20,7 @@ This function can display the persistence result as a barcode: .. plot:: :include-source: + import matplotlib.pyplot as plot import gudhi off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' @@ -29,7 +30,7 @@ This function can display the persistence result as a barcode: simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) diag = simplex_tree.persistence(min_persistence=0.4) - plot = gudhi.plot_persistence_barcode(diag) + gudhi.plot_persistence_barcode(diag) plot.show() Show persistence as a diagram @@ -43,14 +44,15 @@ This function can display the persistence result as a diagram: .. plot:: :include-source: + import matplotlib.pyplot as plot import gudhi # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method persistence_file=gudhi.__root_source_dir__ + \ '/data/persistence_diagram/rips_on_tore3D_1307.pers' - plt = gudhi.plot_persistence_diagram(persistence_file=persistence_file, + gudhi.plot_persistence_diagram(persistence_file=persistence_file, legend=True) - plt.show() + plot.show() Persistence density ------------------- @@ -63,11 +65,12 @@ If you want more information on a specific dimension, for instance: .. plot:: :include-source: + import matplotlib.pyplot as plot import gudhi # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method persistence_file=gudhi.__root_source_dir__ + \ '/data/persistence_diagram/rips_on_tore3D_1307.pers' - plt = gudhi.plot_persistence_density(persistence_file=persistence_file, + gudhi.plot_persistence_density(persistence_file=persistence_file, max_intervals=0, dimension=1, legend=True) - plt.show() + plot.show() diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index b8f283b3..4079a469 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi import argparse +import matplotlib.pyplot as plot +import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -60,8 +61,8 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index 610ba44f..0eedd140 100755 --- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi import argparse +import matplotlib.pyplot as plot +import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -75,8 +76,8 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index 7587b732..1fe55737 100755 --- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi import argparse +import matplotlib.pyplot as plot +import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -74,8 +75,8 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/python/example/gudhi_graphical_tools_example.py b/src/python/example/gudhi_graphical_tools_example.py index 3b0ca54d..37ecbf53 100755 --- a/src/python/example/gudhi_graphical_tools_example.py +++ b/src/python/example/gudhi_graphical_tools_example.py @@ -1,5 +1,6 @@ #!/usr/bin/env python +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -29,15 +30,24 @@ persistence = [ (0, (0.0, 1.0)), ] gudhi.plot_persistence_barcode(persistence) +plot.show() print("#####################################################################") print("Show diagram persistence example") -pplot = gudhi.plot_persistence_diagram(persistence) -pplot.show() +gudhi.plot_persistence_diagram(persistence) +plot.show() print("#####################################################################") print("Show diagram persistence example with a confidence band") -pplot = gudhi.plot_persistence_diagram(persistence, band=0.2) -pplot.show() +gudhi.plot_persistence_diagram(persistence, band=0.2) +plot.show() + +print("#####################################################################") +print("Show barcode and diagram persistence side by side example") +fig, axes = plot.subplots(nrows=1, ncols=2) +gudhi.plot_persistence_barcode(persistence, axes = axes[0]) +gudhi.plot_persistence_diagram(persistence, axes = axes[1]) +fig.suptitle("barcode versus diagram") +plot.show() diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 9cb855cd..c692e66f 100755 --- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi import argparse +import matplotlib.pyplot as plot +import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -70,5 +71,6 @@ if is_file_perseus(args.file): print(periodic_cubical_complex.betti_numbers()) if args.no_barcode == False: gudhi.plot_persistence_barcode(diag) + plot.show() else: print(args.file, "is not a valid perseus style file") diff --git a/src/python/example/plot_alpha_complex.py b/src/python/example/plot_alpha_complex.py new file mode 100755 index 00000000..99c18a7c --- /dev/null +++ b/src/python/example/plot_alpha_complex.py @@ -0,0 +1,37 @@ +#!/usr/bin/env python + +import numpy as np +import gudhi +ac = gudhi.AlphaComplex(off_file='../../data/points/tore3D_1307.off') +st = ac.create_simplex_tree() +points = np.array([ac.get_point(i) for i in range(st.num_vertices())]) +# We want to plot the alpha-complex with alpha=0.1. +# We are only going to plot the triangles +triangles = np.array([s[0] for s in st.get_skeleton(2) if len(s[0])==3 and s[1] <= .1]) + +# First possibility: plotly +import plotly.graph_objects as go +fig = go.Figure(data=[ + go.Mesh3d( + x=points[:,0], + y=points[:,1], + z=points[:,2], + i = triangles[:,0], + j = triangles[:,1], + k = triangles[:,2], + ) +]) +fig.show() + +# Second possibility: matplotlib +from mpl_toolkits.mplot3d import Axes3D +import matplotlib.pyplot as plt +fig = plt.figure() +ax = fig.gca(projection='3d') +ax.plot_trisurf(points[:,0], points[:,1], points[:,2], triangles=triangles) +plt.show() + +# Third possibility: mayavi +from mayavi import mlab +mlab.triangular_mesh(points[:,0], points[:,1], points[:,2], triangles); +mlab.show() diff --git a/src/python/example/plot_rips_complex.py b/src/python/example/plot_rips_complex.py new file mode 100755 index 00000000..1c878db1 --- /dev/null +++ b/src/python/example/plot_rips_complex.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python + +import numpy as np +import gudhi +points = np.array(gudhi.read_off('../../data/points/Kl.off')) +rc = gudhi.RipsComplex(points=points, max_edge_length=.2) +st = rc.create_simplex_tree(max_dimension=2) +# We are only going to plot the triangles +triangles = np.array([s[0] for s in st.get_skeleton(2) if len(s[0])==3]) + +# First possibility: plotly +import plotly.graph_objects as go +fig = go.Figure(data=[ + go.Mesh3d( + # Use the first 3 coordinates, but we could as easily pick others + x=points[:,0], + y=points[:,1], + z=points[:,2], + i = triangles[:,0], + j = triangles[:,1], + k = triangles[:,2], + ) +]) +fig.show() + +# Second possibility: matplotlib +from mpl_toolkits.mplot3d import Axes3D +import matplotlib.pyplot as plt +fig = plt.figure() +ax = fig.gca(projection='3d') +ax.plot_trisurf(points[:,0], points[:,1], points[:,2], triangles=triangles) +plt.show() + +# Third possibility: mayavi +# (this may take a while) +from mayavi import mlab +mlab.triangular_mesh(points[:,0], points[:,1], points[:,2], triangles); +mlab.show() diff --git a/src/python/example/plot_simplex_tree_dim012.py b/src/python/example/plot_simplex_tree_dim012.py new file mode 100755 index 00000000..5b962131 --- /dev/null +++ b/src/python/example/plot_simplex_tree_dim012.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python +import numpy as np +import gudhi + +# Coordinates of the points +points=np.array([[0,0,0],[1,0,0],[0,1,0],[0,0,1],[1,1,1],[1,1,0],[0,1,1]]) +# Build the simplicial complex with a tetrahedon, an edge and an isolated vertex +cplx=gudhi.SimplexTree() +cplx.insert([1,2,3,5]) +cplx.insert([4,6]) +cplx.insert([0]) +# List of triangles (point indices) +triangles = np.array([s[0] for s in cplx.get_skeleton(2) if len(s[0])==3]) +# List of edges (point coordinates) +edges = [] +for s in cplx.get_skeleton(1): + e = s[0] + if len(e) == 2: + edges.append(points[[e[0],e[1]]]) + +## With plotly +import plotly.graph_objects as go +# Plot triangles +f2 = go.Mesh3d( + x=points[:,0], + y=points[:,1], + z=points[:,2], + i = triangles[:,0], + j = triangles[:,1], + k = triangles[:,2], + ) +# Plot points +f0 = go.Scatter3d(x=points[:,0], y=points[:,1], z=points[:,2], mode="markers") +data = [f2, f0] +# Plot edges +for pts in edges: + seg = go.Scatter3d(x=pts[:,0],y=pts[:,1],z=pts[:,2],mode="lines",line=dict(color='green')) + data.append(seg) +fig = go.Figure(data=data,layout=dict(showlegend=False)) +# By default plotly would give each edge its own color and legend, that's too much +fig.show() + +## With matplotlib +from mpl_toolkits.mplot3d import Axes3D +from mpl_toolkits.mplot3d.art3d import Line3DCollection +import matplotlib.pyplot as plt +fig = plt.figure() +ax = fig.gca(projection='3d') +# Plot triangles +ax.plot_trisurf(points[:,0], points[:,1], points[:,2], triangles=triangles) +# Plot points +ax.scatter3D(points[:,0], points[:,1], points[:,2]) +# Plot edges +ax.add_collection3d(Line3DCollection(segments=edges)) +plt.show() + +## With mayavi +from mayavi import mlab +# Plot triangles +mlab.triangular_mesh(points[:,0], points[:,1], points[:,2], triangles); +# Plot points +mlab.points3d(points[:,0], points[:,1], points[:,2]) +# Plot edges +for pts in edges: + mlab.plot3d(pts[:,0],pts[:,1],pts[:,2],tube_radius=None) +mlab.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 3571580b..1acb187c 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -1,8 +1,9 @@ #!/usr/bin/env python -import gudhi import sys import argparse +import matplotlib.pyplot as plot +import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -83,5 +84,5 @@ invert_diag = [ ] if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(invert_diag, band=args.band) + plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 0b9a9ba9..79ccca96 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi import argparse +import matplotlib.pyplot as plot +import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -59,5 +60,5 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py index 2b335bba..b9074cf9 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi import argparse +import matplotlib.pyplot as plot +import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -64,8 +65,8 @@ with open(args.file, "r") as f: print(simplex_tree.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/python/example/rips_persistence_diagram.py b/src/python/example/rips_persistence_diagram.py index f5897d7b..2a90b4bc 100755 --- a/src/python/example/rips_persistence_diagram.py +++ b/src/python/example/rips_persistence_diagram.py @@ -1,5 +1,6 @@ #!/usr/bin/env python +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -26,5 +27,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1) diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0) print("diag=", diag) -pplot = gudhi.plot_persistence_diagram(diag) -pplot.show() +gudhi.plot_persistence_diagram(diag) +plot.show() diff --git a/src/python/example/sparse_rips_persistence_diagram.py b/src/python/example/sparse_rips_persistence_diagram.py index 671d5e34..410a6a86 100755 --- a/src/python/example/sparse_rips_persistence_diagram.py +++ b/src/python/example/sparse_rips_persistence_diagram.py @@ -1,5 +1,6 @@ #!/usr/bin/env python +import matplotlib.pyplot as plot import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -28,5 +29,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=2) diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0) print("diag=", diag) -pplot = gudhi.plot_persistence_diagram(diag) -pplot.show() +gudhi.plot_persistence_diagram(diag) +plot.show() diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py index 456bc9eb..f0df2189 100755 --- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py @@ -1,7 +1,8 @@ #!/usr/bin/env python -import gudhi import argparse +import matplotlib.pyplot as plot +import gudhi """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. @@ -56,8 +57,8 @@ with open(args.file, "r") as f: print(st.betti_numbers()) if args.no_diagram == False: - pplot = gudhi.plot_persistence_diagram(diag, band=args.band) - pplot.show() + gudhi.plot_persistence_diagram(diag, band=args.band) + plot.show() else: print(args.file, "is not a valid OFF file") diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py index 43a00459..c9dab323 100644 --- a/src/python/gudhi/persistence_graphical_tools.py +++ b/src/python/gudhi/persistence_graphical_tools.py @@ -43,27 +43,6 @@ def __min_birth_max_death(persistence, band=0.0): max_death += band return (min_birth, max_death) - -""" -Only 13 colors for the palette -""" -palette = [ - "#ff0000", - "#00ff00", - "#0000ff", - "#00ffff", - "#ff00ff", - "#ffff00", - "#000000", - "#880000", - "#008800", - "#000088", - "#888800", - "#880088", - "#008888", -] - - def plot_persistence_barcode( persistence=[], persistence_file="", @@ -72,6 +51,8 @@ def plot_persistence_barcode( max_barcodes=1000, inf_delta=0.1, legend=False, + colormap=None, + axes=None ): """This function plots the persistence bar code from persistence values list or from a :doc:`persistence file <fileformats>`. @@ -94,14 +75,19 @@ def plot_persistence_barcode( :type inf_delta: float. :param legend: Display the dimension color legend (default is False). :type legend: boolean. - :returns: A matplotlib object containing horizontal bar plot of persistence - (launch `show()` method on it to display it). + :param colormap: A matplotlib-like qualitative colormaps. Default is None + which means :code:`matplotlib.cm.Set1.colors`. + :type colormap: tuple of colors (3-tuple of float between 0. and 1.). + :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on + a new set of axes. + :type axes: `matplotlib.axes.Axes` + :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn. """ try: import matplotlib.pyplot as plt import matplotlib.patches as mpatches - if persistence_file is not "": + if persistence_file != "": if path.isfile(persistence_file): # Reset persistence persistence = [] @@ -115,7 +101,7 @@ def plot_persistence_barcode( print("file " + persistence_file + " not found.") return None - if max_barcodes is not 1000: + if max_barcodes != 1000: print("Deprecated parameter. It has been replaced by max_intervals") max_intervals = max_barcodes @@ -126,6 +112,11 @@ def plot_persistence_barcode( key=lambda life_time: life_time[1][1] - life_time[1][0], reverse=True, )[:max_intervals] + + if colormap == None: + colormap = plt.cm.Set1.colors + if axes == None: + fig, axes = plt.subplots(1, 1) persistence = sorted(persistence, key=lambda birth: birth[1][0]) @@ -140,41 +131,43 @@ def plot_persistence_barcode( for interval in reversed(persistence): if float(interval[1][1]) != float("inf"): # Finite death case - plt.barh( + axes.barh( ind, (interval[1][1] - interval[1][0]), height=0.8, left=interval[1][0], alpha=alpha, - color=palette[interval[0]], + color=colormap[interval[0]], linewidth=0, ) else: # Infinite death case for diagram to be nicer - plt.barh( + axes.barh( ind, (infinity - interval[1][0]), height=0.8, left=interval[1][0], alpha=alpha, - color=palette[interval[0]], + color=colormap[interval[0]], linewidth=0, ) ind = ind + 1 if legend: dimensions = list(set(item[0] for item in persistence)) - plt.legend( + axes.legend( handles=[ - mpatches.Patch(color=palette[dim], label=str(dim)) + mpatches.Patch(color=colormap[dim], label=str(dim)) for dim in dimensions ], loc="lower right", ) - plt.title("Persistence barcode") + + axes.set_title("Persistence barcode") + # Ends plot on infinity value and starts a little bit before min_birth - plt.axis([axis_start, infinity, 0, ind]) - return plt + axes.axis([axis_start, infinity, 0, ind]) + return axes except ImportError: print("This function is not available, you may be missing matplotlib.") @@ -189,6 +182,8 @@ def plot_persistence_diagram( max_plots=1000, inf_delta=0.1, legend=False, + colormap=None, + axes=None ): """This function plots the persistence diagram from persistence values list or from a :doc:`persistence file <fileformats>`. @@ -213,14 +208,19 @@ def plot_persistence_diagram( :type inf_delta: float. :param legend: Display the dimension color legend (default is False). :type legend: boolean. - :returns: A matplotlib object containing diagram plot of persistence - (launch `show()` method on it to display it). + :param colormap: A matplotlib-like qualitative colormaps. Default is None + which means :code:`matplotlib.cm.Set1.colors`. + :type colormap: tuple of colors (3-tuple of float between 0. and 1.). + :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on + a new set of axes. + :type axes: `matplotlib.axes.Axes` + :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn. """ try: import matplotlib.pyplot as plt import matplotlib.patches as mpatches - if persistence_file is not "": + if persistence_file != "": if path.isfile(persistence_file): # Reset persistence persistence = [] @@ -234,7 +234,7 @@ def plot_persistence_diagram( print("file " + persistence_file + " not found.") return None - if max_plots is not 1000: + if max_plots != 1000: print("Deprecated parameter. It has been replaced by max_intervals") max_intervals = max_plots @@ -246,6 +246,11 @@ def plot_persistence_diagram( reverse=True, )[:max_intervals] + if colormap == None: + colormap = plt.cm.Set1.colors + if axes == None: + fig, axes = plt.subplots(1, 1) + (min_birth, max_death) = __min_birth_max_death(persistence, band) delta = (max_death - min_birth) * inf_delta # Replace infinity values with max_death + delta for diagram to be more @@ -256,44 +261,44 @@ def plot_persistence_diagram( # line display of equation : birth = death x = np.linspace(axis_start, infinity, 1000) # infinity line and text - plt.plot(x, x, color="k", linewidth=1.0) - plt.plot(x, [infinity] * len(x), linewidth=1.0, color="k", alpha=alpha) - plt.text(axis_start, infinity, r"$\infty$", color="k", alpha=alpha) + axes.plot(x, x, color="k", linewidth=1.0) + axes.plot(x, [infinity] * len(x), linewidth=1.0, color="k", alpha=alpha) + axes.text(axis_start, infinity, r"$\infty$", color="k", alpha=alpha) # bootstrap band if band > 0.0: - plt.fill_between(x, x, x + band, alpha=alpha, facecolor="red") + axes.fill_between(x, x, x + band, alpha=alpha, facecolor="red") # Draw points in loop for interval in reversed(persistence): if float(interval[1][1]) != float("inf"): # Finite death case - plt.scatter( + axes.scatter( interval[1][0], interval[1][1], alpha=alpha, - color=palette[interval[0]], + color=colormap[interval[0]], ) else: # Infinite death case for diagram to be nicer - plt.scatter( - interval[1][0], infinity, alpha=alpha, color=palette[interval[0]] + axes.scatter( + interval[1][0], infinity, alpha=alpha, color=colormap[interval[0]] ) if legend: dimensions = list(set(item[0] for item in persistence)) - plt.legend( + axes.legend( handles=[ - mpatches.Patch(color=palette[dim], label=str(dim)) + mpatches.Patch(color=colormap[dim], label=str(dim)) for dim in dimensions ] ) - plt.title("Persistence diagram") - plt.xlabel("Birth") - plt.ylabel("Death") + axes.set_xlabel("Birth") + axes.set_ylabel("Death") # Ends plot on infinity value and starts a little bit before min_birth - plt.axis([axis_start, infinity, axis_start, infinity + delta]) - return plt + axes.axis([axis_start, infinity, axis_start, infinity + delta]) + axes.set_title("Persistence diagram") + return axes except ImportError: print("This function is not available, you may be missing matplotlib.") @@ -308,6 +313,7 @@ def plot_persistence_density( dimension=None, cmap=None, legend=False, + axes=None ): """This function plots the persistence density from persistence values list or from a :doc:`persistence file <fileformats>`. Be @@ -346,14 +352,16 @@ def plot_persistence_density( :type cmap: cf. matplotlib colormap. :param legend: Display the color bar values (default is False). :type legend: boolean. - :returns: A matplotlib object containing diagram plot of persistence - (launch `show()` method on it to display it). + :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on + a new set of axes. + :type axes: `matplotlib.axes.Axes` + :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn. """ try: import matplotlib.pyplot as plt from scipy.stats import kde - if persistence_file is not "": + if persistence_file != "": if dimension is None: # All dimension case dimension = -1 @@ -390,9 +398,15 @@ def plot_persistence_density( birth = persistence_dim[:, 0] death = persistence_dim[:, 1] + # default cmap value cannot be done at argument definition level as matplotlib is not yet defined. + if cmap is None: + cmap = plt.cm.hot_r + if axes == None: + fig, axes = plt.subplots(1, 1) + # line display of equation : birth = death x = np.linspace(death.min(), birth.max(), 1000) - plt.plot(x, x, color="k", linewidth=1.0) + axes.plot(x, x, color="k", linewidth=1.0) # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents k = kde.gaussian_kde([birth, death], bw_method=bw_method) @@ -402,19 +416,16 @@ def plot_persistence_density( ] zi = k(np.vstack([xi.flatten(), yi.flatten()])) - # default cmap value cannot be done at argument definition level as matplotlib is not yet defined. - if cmap is None: - cmap = plt.cm.hot_r # Make the plot - plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap) + axes.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap) if legend: - plt.colorbar() + axes.colorbar() - plt.title("Persistence density") - plt.xlabel("Birth") - plt.ylabel("Death") - return plt + axes.set_xlabel("Birth") + axes.set_ylabel("Death") + axes.set_title("Persistence density") + return axes except ImportError: print( |